rs9966950

chr18-11304692-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0461 in 152,268 control chromosomes in the GnomAD database, including 220 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.046 (220 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0462 AC: 7022 AN: 152148 Hom.: 220 Cov.: 32

Gnomad AFR AF: 0.0627

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.0821

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0520

Gnomad FIN AF: 0.00876

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0456

Gnomad OTH AF: 0.0449

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0461 AC: 7024 AN: 152268 Hom.: 220 Cov.: 32 AF XY: 0.0446 AC XY: 3322 AN XY: 74452

Gnomad4 AFR AF: 0.0625

Gnomad4 AMR AF: 0.0373

Gnomad4 ASJ AF: 0.0821

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0524

Gnomad4 FIN AF: 0.00876

Gnomad4 NFE AF: 0.0456

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0412 Hom.: 13

Bravo AF: 0.0482

Asia WGS AF: 0.0240 AC: 84 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.9
Dann	Benign	0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9966950; hg19: chr18-11304691;